Starting phenix.real_space_refine on Tue Dec 12 06:34:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/12_2023/6cij_7480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/12_2023/6cij_7480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/12_2023/6cij_7480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/12_2023/6cij_7480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/12_2023/6cij_7480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/12_2023/6cij_7480.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 209 5.49 5 S 109 5.16 5 C 12241 2.51 5 N 3602 2.21 5 O 4248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C GLU 959": "OE1" <-> "OE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20413 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4921 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 588} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4946 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 590} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "I" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1225 Classifications: {'DNA': 60} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 59} Chain: "N" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 910 Classifications: {'peptide': 133} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 610 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2643 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2652 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 845 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2590 SG CYS A 727 97.498 23.316 70.665 1.00 75.34 S ATOM 2611 SG CYS A 730 98.266 20.427 68.704 1.00 76.35 S ATOM 7544 SG CYS C 727 62.510 83.572 69.781 1.00 72.00 S ATOM 7565 SG CYS C 730 61.451 86.448 68.000 1.00 75.09 S Time building chain proxies: 13.12, per 1000 atoms: 0.64 Number of scatterers: 20413 At special positions: 0 Unit cell: (160.5, 109.14, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 109 16.00 P 209 15.00 O 4248 8.00 N 3602 7.00 C 12241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.80 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 40.5% alpha, 17.9% beta 93 base pairs and 160 stacking pairs defined. Time for finding SS restraints: 7.89 Creating SS restraints... Processing helix chain 'A' and resid 403 through 423 removed outlier: 5.800A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 3.567A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.571A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.595A pdb=" N CYS A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.738A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.605A pdb=" N ASN A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.536A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 894 removed outlier: 3.794A pdb=" N ARG A 894 " --> pdb=" O PRO A 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 924 removed outlier: 3.543A pdb=" N ASN A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.837A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.717A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.717A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'C' and resid 400 through 421 removed outlier: 5.433A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 492 removed outlier: 3.708A pdb=" N LYS C 489 " --> pdb=" O TYR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.639A pdb=" N LEU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 510 No H-bonds generated for 'chain 'C' and resid 508 through 510' Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.560A pdb=" N CYS C 651 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 735 through 739 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 4.013A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 removed outlier: 4.070A pdb=" N ARG C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 873 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 removed outlier: 3.676A pdb=" N ASN C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.647A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.618A pdb=" N ALA C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.722A pdb=" N GLN C 962 " --> pdb=" O SER C 958 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 996 through 1002 removed outlier: 3.588A pdb=" N GLN C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.635A pdb=" N VAL N 20 " --> pdb=" O TYR N 16 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR N 22 " --> pdb=" O PHE N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 43 Processing helix chain 'N' and resid 44 through 49 removed outlier: 3.502A pdb=" N ARG N 48 " --> pdb=" O LYS N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 66 removed outlier: 4.210A pdb=" N MET N 63 " --> pdb=" O LYS N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 72 Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 121 through 134 Processing helix chain 'N' and resid 142 through 158 removed outlier: 4.269A pdb=" N LYS N 147 " --> pdb=" O PRO N 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.586A pdb=" N HIS D 313 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.607A pdb=" N LYS B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.757A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 688 " --> pdb=" O GLU A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.805A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 641 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.805A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 595 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA5, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.519A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.519A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.784A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.683A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.780A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 78 removed outlier: 3.599A pdb=" N HIS D 94 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.082A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB5, first strand: chain 'D' and resid 208 through 210 Processing sheet with id=AB6, first strand: chain 'D' and resid 208 through 210 removed outlier: 4.580A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 235 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 250 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 263 through 267 removed outlier: 4.943A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.510A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 22 through 24 removed outlier: 3.775A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 56 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 94 removed outlier: 4.287A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 112 through 115 removed outlier: 6.408A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.646A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 156 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AC5, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.632A pdb=" N TYR B 234 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.985A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 229 hydrogen bonds 450 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 160 stacking parallelities Total time for adding SS restraints: 10.72 Time building geometry restraints manager: 14.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5655 1.34 - 1.46: 4775 1.46 - 1.57: 10285 1.57 - 1.69: 415 1.69 - 1.81: 165 Bond restraints: 21295 Sorted by residual: bond pdb=" C3' DT J 3 " pdb=" O3' DT J 3 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C LYS A 890 " pdb=" O LYS A 890 " ideal model delta sigma weight residual 1.244 1.231 0.012 1.00e-02 1.00e+04 1.55e+00 bond pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CA LYS A 890 " pdb=" C LYS A 890 " ideal model delta sigma weight residual 1.520 1.535 -0.014 1.23e-02 6.61e+03 1.36e+00 bond pdb=" C3' DA F 32 " pdb=" O3' DA F 32 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 21290 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.20: 1206 105.20 - 112.40: 11139 112.40 - 119.59: 6547 119.59 - 126.79: 9983 126.79 - 133.98: 822 Bond angle restraints: 29697 Sorted by residual: angle pdb=" N GLN A 456 " pdb=" CA GLN A 456 " pdb=" C GLN A 456 " ideal model delta sigma weight residual 112.45 104.02 8.43 1.39e+00 5.18e-01 3.68e+01 angle pdb=" C GLY A 457 " pdb=" N ARG A 458 " pdb=" CA ARG A 458 " ideal model delta sigma weight residual 122.59 114.89 7.70 1.57e+00 4.06e-01 2.41e+01 angle pdb=" N ARG A 558 " pdb=" CA ARG A 558 " pdb=" C ARG A 558 " ideal model delta sigma weight residual 109.96 101.89 8.07 1.68e+00 3.54e-01 2.31e+01 angle pdb=" N LYS A 890 " pdb=" CA LYS A 890 " pdb=" C LYS A 890 " ideal model delta sigma weight residual 112.75 118.40 -5.65 1.36e+00 5.41e-01 1.73e+01 angle pdb=" N TRP B 172 " pdb=" CA TRP B 172 " pdb=" C TRP B 172 " ideal model delta sigma weight residual 111.71 116.26 -4.55 1.15e+00 7.56e-01 1.57e+01 ... (remaining 29692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 11302 35.10 - 70.20: 914 70.20 - 105.31: 25 105.31 - 140.41: 1 140.41 - 175.51: 2 Dihedral angle restraints: 12244 sinusoidal: 6307 harmonic: 5937 Sorted by residual: dihedral pdb=" CA PHE N 18 " pdb=" C PHE N 18 " pdb=" N PHE N 19 " pdb=" CA PHE N 19 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ALA N 94 " pdb=" C ALA N 94 " pdb=" N PRO N 95 " pdb=" CA PRO N 95 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C4' DC J 9 " pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " pdb=" P DT J 10 " ideal model delta sinusoidal sigma weight residual 220.00 44.49 175.51 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2685 0.045 - 0.091: 422 0.091 - 0.136: 142 0.136 - 0.181: 6 0.181 - 0.226: 6 Chirality restraints: 3261 Sorted by residual: chirality pdb=" CA ARG A 558 " pdb=" N ARG A 558 " pdb=" C ARG A 558 " pdb=" CB ARG A 558 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 890 " pdb=" N LYS A 890 " pdb=" C LYS A 890 " pdb=" CB LYS A 890 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP N 91 " pdb=" N ASP N 91 " pdb=" C ASP N 91 " pdb=" CB ASP N 91 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3258 not shown) Planarity restraints: 3091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 558 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ARG C 558 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG C 558 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 559 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 520 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 521 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ALA C 441 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA C 441 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG C 442 " 0.013 2.00e-02 2.50e+03 ... (remaining 3088 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 221 2.62 - 3.19: 17247 3.19 - 3.76: 32894 3.76 - 4.33: 43345 4.33 - 4.90: 67820 Nonbonded interactions: 161527 Sorted by model distance: nonbonded pdb=" OP2 DT G 42 " pdb="CA CA C1102 " model vdw 2.055 2.510 nonbonded pdb=" NH2 ARG D 212 " pdb=" O GLY D 293 " model vdw 2.203 2.520 nonbonded pdb=" OG1 THR D 308 " pdb=" OD1 ASP D 310 " model vdw 2.214 2.440 nonbonded pdb=" N MET B 1 " pdb=" O ARG B 349 " model vdw 2.215 2.520 nonbonded pdb=" OD1 ASP C 569 " pdb=" OG SER C 996 " model vdw 2.228 2.440 ... (remaining 161522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 395 through 401 or (resid 402 through 403 and (name N or n \ ame CA or name C or name O or name CB )) or resid 404 through 519 or (resid 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 10 \ 06 or (resid 1007 and (name N or name CA or name C or name O or name CB )) or re \ sid 1101 through 1102)) selection = (chain 'C' and ((resid 395 and (name N or name CA or name C or name O or name CB \ )) or resid 396 or (resid 397 and (name N or name CA or name C or name O or nam \ e CB )) or resid 398 through 523 or (resid 524 and (name N or name CA or name C \ or name O or name CB )) or resid 525 through 689 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 1007 or resid 1101 \ through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 335 or resid 341 through 350 or (resid 351 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.030 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 79.450 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.155 Angle : 0.578 8.430 29697 Z= 0.365 Chirality : 0.039 0.226 3261 Planarity : 0.004 0.056 3091 Dihedral : 19.646 175.510 8412 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 2.25 % Allowed : 3.41 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.17), residues: 2021 helix: -0.57 (0.18), residues: 730 sheet: -2.01 (0.27), residues: 346 loop : -2.65 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 829 HIS 0.003 0.000 HIS N 27 PHE 0.011 0.001 PHE A 916 TYR 0.012 0.001 TYR A 805 ARG 0.004 0.000 ARG C 679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 258 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 14 residues processed: 291 average time/residue: 0.4337 time to fit residues: 177.6856 Evaluate side-chains 132 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 2.183 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5390 time to fit residues: 12.5835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 473 ASN A 495 GLN A 505 ASN A 850 ASN A 912 ASN A 978 GLN A 990 HIS C 495 GLN C 809 GLN C 860 GLN ** C 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C 978 GLN C 990 HIS C1000 GLN N 135 ASN D 47 HIS D 94 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.192 Angle : 0.583 8.870 29697 Z= 0.319 Chirality : 0.038 0.211 3261 Planarity : 0.004 0.047 3091 Dihedral : 23.729 175.313 4540 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 8.43 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2021 helix: 0.55 (0.19), residues: 739 sheet: -1.29 (0.28), residues: 357 loop : -2.19 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 893 HIS 0.009 0.001 HIS N 27 PHE 0.012 0.001 PHE B 189 TYR 0.014 0.001 TYR A 805 ARG 0.009 0.001 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 2.030 Fit side-chains outliers start: 18 outliers final: 3 residues processed: 148 average time/residue: 0.3297 time to fit residues: 77.1771 Evaluate side-chains 106 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2052 time to fit residues: 3.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 0.0010 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 912 ASN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21295 Z= 0.246 Angle : 0.582 8.898 29697 Z= 0.319 Chirality : 0.039 0.142 3261 Planarity : 0.004 0.046 3091 Dihedral : 23.891 174.220 4540 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.87 % Allowed : 9.41 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 2021 helix: 0.98 (0.20), residues: 744 sheet: -0.86 (0.29), residues: 349 loop : -1.89 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS D 313 PHE 0.017 0.001 PHE A 418 TYR 0.021 0.001 TYR N 109 ARG 0.005 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 2.127 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 115 average time/residue: 0.3393 time to fit residues: 63.3299 Evaluate side-chains 105 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1952 time to fit residues: 5.6029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.3980 chunk 151 optimal weight: 0.0670 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 192 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21295 Z= 0.151 Angle : 0.545 12.506 29697 Z= 0.296 Chirality : 0.037 0.139 3261 Planarity : 0.003 0.041 3091 Dihedral : 23.804 174.738 4540 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.58 % Allowed : 9.58 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 2021 helix: 1.15 (0.20), residues: 748 sheet: -0.69 (0.28), residues: 352 loop : -1.74 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 893 HIS 0.003 0.000 HIS N 27 PHE 0.023 0.001 PHE B 189 TYR 0.018 0.001 TYR N 109 ARG 0.003 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.906 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 113 average time/residue: 0.3195 time to fit residues: 58.7731 Evaluate side-chains 100 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2115 time to fit residues: 2.9865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 192 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21295 Z= 0.158 Angle : 0.532 9.923 29697 Z= 0.290 Chirality : 0.037 0.132 3261 Planarity : 0.003 0.042 3091 Dihedral : 23.805 174.565 4540 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.64 % Allowed : 10.51 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2021 helix: 1.31 (0.20), residues: 747 sheet: -0.51 (0.28), residues: 358 loop : -1.58 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.010 0.001 HIS N 27 PHE 0.019 0.001 PHE A 418 TYR 0.014 0.001 TYR N 109 ARG 0.004 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 2.096 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 108 average time/residue: 0.3186 time to fit residues: 56.0085 Evaluate side-chains 100 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1929 time to fit residues: 4.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN A 962 GLN C 860 GLN C 912 ASN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21295 Z= 0.262 Angle : 0.582 11.817 29697 Z= 0.314 Chirality : 0.039 0.141 3261 Planarity : 0.004 0.040 3091 Dihedral : 23.919 173.621 4540 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.04 % Allowed : 10.05 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 2021 helix: 1.42 (0.20), residues: 749 sheet: -0.33 (0.29), residues: 337 loop : -1.51 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.006 0.001 HIS N 27 PHE 0.018 0.002 PHE N 105 TYR 0.015 0.001 TYR N 109 ARG 0.004 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.991 Fit side-chains outliers start: 18 outliers final: 2 residues processed: 109 average time/residue: 0.3357 time to fit residues: 58.1866 Evaluate side-chains 96 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2427 time to fit residues: 3.5777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 122 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.160 Angle : 0.544 13.308 29697 Z= 0.293 Chirality : 0.037 0.138 3261 Planarity : 0.003 0.039 3091 Dihedral : 23.839 174.126 4540 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.52 % Allowed : 10.68 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 2021 helix: 1.53 (0.20), residues: 748 sheet: -0.19 (0.29), residues: 343 loop : -1.42 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 893 HIS 0.006 0.000 HIS N 27 PHE 0.035 0.001 PHE B 189 TYR 0.011 0.001 TYR C 909 ARG 0.005 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 2.076 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 100 average time/residue: 0.3267 time to fit residues: 53.1793 Evaluate side-chains 96 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2108 time to fit residues: 3.8722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 168 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 HIS A1000 GLN C 456 GLN C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 21295 Z= 0.506 Angle : 0.712 12.702 29697 Z= 0.380 Chirality : 0.044 0.161 3261 Planarity : 0.005 0.049 3091 Dihedral : 24.166 172.160 4540 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.64 % Allowed : 10.85 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 2021 helix: 1.15 (0.20), residues: 763 sheet: -0.30 (0.29), residues: 325 loop : -1.73 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 893 HIS 0.009 0.002 HIS N 27 PHE 0.039 0.002 PHE B 189 TYR 0.018 0.002 TYR A 485 ARG 0.005 0.001 ARG C 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 2.144 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 0.3408 time to fit residues: 54.4948 Evaluate side-chains 99 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2255 time to fit residues: 5.8162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5878 > 50: distance: 41 - 46: 22.176 distance: 46 - 47: 37.841 distance: 47 - 48: 35.430 distance: 47 - 50: 34.482 distance: 48 - 49: 32.478 distance: 48 - 57: 11.292 distance: 50 - 51: 25.801 distance: 51 - 52: 12.052 distance: 51 - 53: 49.800 distance: 54 - 56: 22.377 distance: 55 - 56: 44.126 distance: 57 - 58: 23.668 distance: 58 - 59: 22.417 distance: 58 - 61: 21.815 distance: 61 - 62: 37.872 distance: 62 - 63: 12.391 distance: 63 - 64: 4.728 distance: 63 - 65: 18.962 distance: 66 - 67: 9.967 distance: 67 - 68: 48.167 distance: 67 - 70: 7.706 distance: 68 - 69: 41.830 distance: 68 - 75: 53.913 distance: 70 - 71: 28.682 distance: 71 - 72: 39.927 distance: 72 - 73: 16.545 distance: 72 - 74: 41.961 distance: 75 - 76: 45.222 distance: 75 - 81: 44.439 distance: 76 - 77: 39.710 distance: 76 - 79: 56.324 distance: 77 - 78: 36.373 distance: 77 - 82: 37.752 distance: 79 - 80: 51.206 distance: 80 - 81: 28.887 distance: 82 - 83: 40.727 distance: 83 - 84: 38.749 distance: 83 - 86: 38.810 distance: 84 - 85: 13.679 distance: 84 - 91: 45.738 distance: 87 - 88: 18.155 distance: 88 - 89: 50.724 distance: 89 - 90: 20.508 distance: 91 - 92: 38.522 distance: 91 - 97: 26.793 distance: 92 - 93: 53.530 distance: 92 - 95: 15.821 distance: 93 - 94: 22.801 distance: 93 - 98: 3.380 distance: 96 - 97: 30.310 distance: 98 - 99: 41.781 distance: 99 - 100: 5.327 distance: 99 - 102: 31.076 distance: 100 - 101: 45.650 distance: 102 - 103: 13.134 distance: 103 - 104: 27.860 distance: 103 - 105: 5.166 distance: 106 - 107: 4.850 distance: 107 - 110: 41.110 distance: 108 - 109: 29.857 distance: 108 - 112: 10.011 distance: 110 - 111: 18.493 distance: 112 - 113: 57.817 distance: 113 - 114: 64.870 distance: 113 - 116: 14.436 distance: 114 - 115: 53.055 distance: 114 - 121: 65.155 distance: 115 - 135: 34.269 distance: 116 - 117: 12.381 distance: 117 - 118: 68.043 distance: 118 - 120: 39.091 distance: 121 - 122: 56.217 distance: 122 - 123: 56.800 distance: 122 - 125: 50.125 distance: 123 - 129: 35.632 distance: 125 - 126: 40.541 distance: 126 - 127: 40.056 distance: 126 - 128: 10.679